Actually Emscripten outputs a strict subset of JS dubbed asm.js. Using this allows some really significant speed improvements in execution, due to simplified type checking.
My understanding then is that for certain things this could well be faster than a hand written Javascript port.
asm.js can quite easily be optimized, but V8 is not yet optimized for it. So depending on the case it might run faster or slower depending on what JavaScript engine is running it.
My understanding then is that for certain things this could well be faster than a hand written Javascript port.